rennero.blogg.se - Vmd atom selection

#VMD ATOM SELECTION SOFTWARE#
#VMD ATOM SELECTION WINDOWS#

Keep in mind that you can save the visualizing state of your system whenever you want by saving a state.vmd file. And as we are simulating bigger and bigger systems in which more and more beads are involved, the previous trick can be adapted to increase the displaying/seeking speed of trajectories by writing representations showing only beads needed for the visualization (head groups of a bilayer for instance). Try it yourself! VMD is really demanding in term of memory an easy trick to decrease the amount needed by VMD is to load structure/trajectories containing only beads needed by your analysis this can easily be done by preprocessing the trajectory using trjconv.

To display all lipids (excluding DPPC) whose heads are interacting with the same specific residues: same resid as ((within 7.0 of (index 531 to 538)) and name NC3 PO4 "GL.*") and not resname DPPC.Īs you can see in the examples, all these keywords can be mixed with the logical links: and, or, not, etc.

To display the water shell around specic residues: within 7.0 of (index 531 to 538).

To show only charged positively charged residues (in Martini): resname LYS ARG.

To get rid of solvent (water/ion beads): not resname W WF ION or WP in case of polarizable water.

To select only backbone beads of a protein: name BB (use "BB.*" or BAS for old versions of FG-to-CG scripts).

To select only lipids: resname POPC, or only part of each lipids: resname POPC and name "C.*.A" "C.*.*.B" "D.*.A" "D.*.B" for lipid tails (C1A,C1B, etc.) and resname POPC and name NC3 PO4 "GL.*" for heads.

More general keywords are implemented to be able to display non-classical-systems (CG systems are part of this second category) you can find them in VMD manual: VMD comes with implemented keywords for all-atom systems ("protein", "chain", "hydrogen", "solvent", etc.). VMD adopted a representation-philosophy: for any set of atoms/molecules/protein chains we want to display or analyze, we need to select this set through a "representation" defined by keywords related to this set (somewhat similar to make_ndx). A good tutorial for Bendix can be found here: Additionally, Tcl scripts are presented that assist with the visualization of CG systems these scripts, as well as extended help, are available on the Martini websiteĪn additional, very usefull tool for displaying CG (Martini) structures in VMD is Bendix. In this module, we explain some of the vmd commands that can be used to visualize the CG systems. VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Then you can see the atom number of each atom in one display, instead of highlighting one by one in VMD.Martini tutorials: visualizing Martini systems using VMD

#VMD ATOM SELECTION WINDOWS#

In the "Display types" windows on the left, you can turn on Label which will show the atom numbers of each atom in the display: For example, Avogadro can read output files from many quantum chemistry codes and visualise the structure. For those, there are many other visualisation programs which would be easier to use I believe.

#VMD ATOM SELECTION SOFTWARE#

If you are calculating NMR, I assume you are using a small system (~50 atoms max) and using some quantum chemistry software like Gaussian or Orca. You can go to the "Selections" tab in the Graphical Representations window to see all of the options available.Īs an aside, VMD's main strength is visualising a large number of atoms, it is mainly targeted at molecular dynamics. VMD can also select atoms in many other ways.

(I am using a large system with ~ 3000 atoms so there are a lot of atoms on the screen with smaller systems, you would be able to see the highlighted atom even more clearly.)

You can see that atom number 10 is now clearly visible among all others. Alternatively you can change the colouring scheme to highlight atom.

Then change drawing method to "VDW" to highlight that atom (it will become bigger). 3) Click on "Create Rep" button and a new representation will be created with the atom selection "all"ĭelete "all" and type "index 10" to select only atom 10 for the visualization, then click "Apply". I would recommend using Lines or CPK as drawing method for the main system (selected atoms = "all"), as this gives small atom size in display. 1) Open the file with VMD 2) From the menu bar go to Graphics > Representations. You do not need atomselect to do this in VMD, you can do this from the GUI as well.